forked from lijiext/lammps
149 lines
5.1 KiB
Plaintext
149 lines
5.1 KiB
Plaintext
.. index:: fix tmd
|
|
|
|
fix tmd command
|
|
===============
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
fix ID group-ID tmd rho_final file1 N file2
|
|
|
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
|
* tmd = style name of this fix command
|
|
* rho_final = desired value of rho at the end of the run (distance units)
|
|
* file1 = filename to read target structure from
|
|
* N = dump TMD statistics every this many timesteps, 0 = no dump
|
|
* file2 = filename to write TMD statistics to (only needed if N > 0)
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
fix 1 all nve
|
|
fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
Perform targeted molecular dynamics (TMD) on a group of atoms. A
|
|
holonomic constraint is used to force the atoms to move towards (or
|
|
away from) the target configuration. The parameter "rho" is
|
|
monotonically decreased (or increased) from its initial value to
|
|
rho_final at the end of the run.
|
|
|
|
Rho has distance units and is a measure of the root-mean-squared
|
|
distance (RMSD) between the current configuration of the atoms in the
|
|
group and the target coordinates listed in file1. Thus a value of
|
|
rho_final = 0.0 means move the atoms all the way to the final
|
|
structure during the course of the run.
|
|
|
|
The target file1 can be ASCII text or a gzipped text file (detected by
|
|
a .gz suffix). The format of the target file1 is as follows:
|
|
|
|
.. parsed-literal::
|
|
|
|
0.0 25.0 xlo xhi
|
|
0.0 25.0 ylo yhi
|
|
0.0 25.0 zlo zhi
|
|
125 24.97311 1.69005 23.46956 0 0 -1
|
|
126 1.94691 2.79640 1.92799 1 0 0
|
|
127 0.15906 3.46099 0.79121 1 0 0
|
|
...
|
|
|
|
The first 3 lines may or may not be needed, depending on the format of
|
|
the atoms to follow. If image flags are included with the atoms, the
|
|
1st 3 lo/hi lines must appear in the file. If image flags are not
|
|
included, the 1st 3 lines should not appear. The 3 lines contain the
|
|
simulation box dimensions for the atom coordinates, in the same format
|
|
as in a LAMMPS data file (see the :doc:`read_data <read_data>` command).
|
|
|
|
The remaining lines each contain an atom ID and its target x,y,z
|
|
coordinates. The atom lines (all or none of them) can optionally be
|
|
followed by 3 integer values: nx,ny,nz. For periodic dimensions, they
|
|
specify which image of the box the atom is considered to be in, i.e. a
|
|
value of N (positive or negative) means add N times the box length to
|
|
the coordinate to get the true value.
|
|
|
|
The atom lines can be listed in any order, but every atom in the group
|
|
must be listed in the file. Atoms not in the fix group may also be
|
|
listed; they will be ignored.
|
|
|
|
TMD statistics are written to file2 every N timesteps, unless N is
|
|
specified as 0, which means no statistics.
|
|
|
|
The atoms in the fix tmd group should be integrated (via a fix nve,
|
|
nvt, npt) along with other atoms in the system.
|
|
|
|
Restarts can be used with a fix tmd command. For example, imagine a
|
|
10000 timestep run with a rho_initial = 11 and a rho_final = 1. If a
|
|
restart file was written after 2000 time steps, then the configuration
|
|
in the file would have a rho value of 9. A new 8000 time step run
|
|
could be performed with the same rho_final = 1 to complete the
|
|
conformational change at the same transition rate. Note that for
|
|
restarted runs, the name of the TMD statistics file should be changed
|
|
to prevent it being overwritten.
|
|
|
|
For more information about TMD, see :ref:`(Schlitter1) <Schlitter1>` and
|
|
:ref:`(Schlitter2) <Schlitter2>`.
|
|
|
|
Restart, fix_modify, output, run start/stop, minimize info
|
|
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
|
|
|
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
|
|
are relevant to this fix. No global or per-atom quantities are stored
|
|
by this fix for access by various :ref:`output commands <howto_15>`.
|
|
|
|
This fix can ramp its rho parameter over multiple runs, using the
|
|
*start* and *stop* keywords of the :doc:`run <run>` command. See the
|
|
:doc:`run <run>` command for details of how to do this.
|
|
|
|
This fix is not invoked during :doc:`energy minimization <minimize>`.
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
|
|
|
|
All TMD fixes must be listed in the input script after all integrator
|
|
fixes (nve, nvt, npt) are applied. This ensures that atoms are moved
|
|
before their positions are corrected to comply with the constraint.
|
|
|
|
Atoms that have a TMD fix applied should not be part of a group to
|
|
which a SHAKE fix is applied. This is because LAMMPS assumes there
|
|
are not multiple competing holonomic constraints applied to the same
|
|
atoms.
|
|
|
|
To read gzipped target files, you must compile LAMMPS with the
|
|
-DLAMMPS_GZIP option - see the :ref:`Making LAMMPS <start_2>` section of the documentation.
|
|
|
|
**Related commands:** none
|
|
|
|
**Default:** none
|
|
|
|
|
|
----------
|
|
|
|
|
|
.. _Schlitter1:
|
|
|
|
|
|
|
|
**(Schlitter1)** Schlitter, Swegat, Mulders, "Distance-type reaction
|
|
coordinates for modelling activated processes", J Molecular Modeling,
|
|
7, 171-177 (2001).
|
|
|
|
.. _Schlitter2:
|
|
|
|
|
|
|
|
**(Schlitter2)** Schlitter and Klahn, "The free energy of a reaction
|
|
coordinate at multiple constraints: a concise formulation", Molecular
|
|
Physics, 101, 3439-3443 (2003).
|
|
|
|
|
|
.. _lws: http://lammps.sandia.gov
|
|
.. _ld: Manual.html
|
|
.. _lc: Section_commands.html#comm
|